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If you’ve watched any major-college football or basketball games this year, you’ve probably seen the NCAA commercial touting the success of Division I black male athletes, who graduate at higher rates than African-American students over all.

In fact, more than 70 percent of big-time football and basketball players completed their degrees within six years of enrolling, according to the NCAA’s latest Graduation Success Rates.

But barely 50 percent of black male athletes in the six most powerful conferences graduate in that time, according to a newly released analysis of federal graduation-rate data by the Center for the Study of Race and Equity in Education at the University of Pennsylvania.

The situation is even more bleak at certain Bowl Championship Series programs. Fewer than one in three black male athletes at Iowa State, South Florida, Arizona, and Arkansas graduate in six years, the report says.

And some of the nation’s most elite programs, including Florida (34 percent) and Indiana (36 percent), aren’t doing much better.

On average, just 42 percent of black male athletes at Alabama, Auburn, Florida, and LSU—the most recent national champions in football—graduate within six years, says the report, “Black Male Student-Athletes and Racial Inequities in NCAA Division I College Sports.”

Among the six prominent leagues, the Southeastern Conference has the lowest average six-year graduation rate for black male athletes, at 45.4 percent. That is 9.5 percent lower than the rate for the Big East Conference, which fared the best of the six (Nos. 2 to 5 were the Atlantic Coast Conference, Big Ten, Pac-12, and Big 12).

There were a few bright spots, including at Notre Dame (where 81 percent of players graduated, according to the most recent federal data) and Stanford (where 68 percent graduated). The Fighting Irish play for the national title next month, and Stanford has also earned a BCS berth.

But persistently low graduation rates at the vast majority of the 76 biggest-revenue sports programs should be a wake-up call for NCAA institutions, says the report’s lead author, Shaun R. Harper, who is an associate professor in Penn’s Graduate School of Education and is director of the Center for the Study of Race and Equity in Education.

“These colleges and conferences make millions of dollars on the backs of black male student-athletes,” Mr. Harper said in an interview. “The least they can do is graduate them and make sure that they’re prepared for viable postcollege options beyond the NFL and the NBA.”

Plenty of scholars have examined racial disparities in sport. The Penn center’s report stands out because it aggregates graduation rates by race in the biggest and richest conferences.

One of the report’s limitations is its reliance on the U.S. Department of Education’s graduation-rate figures, which do not account for students who transfer to other institutions. The NCAA’s Graduation Success Rate provides a more accurate accounting of players’ persistence through college because it counts transfers. But the authors argue there is no evidence that black male athletes are any more or less likely than teammates in other racial groups to transfer.

If you read nothing else in the report, be sure to check out the recommendations for improving racial gaps (starting on Page 18). The ideas there make many of the recent headlines we’ve seen, including those about conference realignment, seem trivial.

Among other suggestions, the report calls on the NCAA to start producing graduation-rate reports that break out data by race, sex, sport, and divisional subsets, which would shed more light on problems (particularly in the power conferences).

The authors, who also include Collin D. Williams Jr. and Horatio W. Blackman, suggest that athletics departments devise strategies for narrowing racial gaps in graduation rates, treating the academic success of black athletes as seriously as they do winning BCS titles.

And they want admissions offices to do more to fill their classes with black men—not just star black athletes.

“If college admissions officers did the kind of things football coaches do, we’re optimistic they could find lots more black undergraduate men for the general student body,” Mr. Harper said.

The report commends Arne Duncan, the U.S. secretary of education, for proposing that teams must graduate at least 40 percent of their players before they are allowed to compete in NCAA championships.

But the authors suggest that programs be required to have adequate black-athlete graduation rates—not just sufficient overall graduation rates—before they can compete in the postseason.

“Teams that sustain racial inequities,” the report says, “should not be rewarded with opportunities to play for NCAA championships.”

Finally, the report says that conferences should give a larger portion of their revenue, including more proceeds from championships, back to member institutions for programs that aim to improve racial equity within and beyond sports.